MRI-Based Deep-Learning Method for Determining Glioma MGMT Promoter Methylation Status

• Published in: American journal of neuroradiology : AJNR Vol. 42; no. 5; pp. 845 - 852
• Main Authors: Yogananda, C.G.B., Shah, B.R., Nalawade, S.S., Murugesan, G.K., Yu, F.F., Pinho, M.C., Wagner, B.C., Mickey, B., Patel, T.R., Fei, B., Madhuranthakam, A.J., Maldjian, J.A.
• Format: Journal Article
• Language: English
• Published: United States American Society of Neuroradiology 01.05.2021
• Subjects: Adult; Adult Brain; Aged; Area Under Curve; Brain Neoplasms - diagnostic imaging; Brain Neoplasms - genetics; Deep Learning; DNA Methylation; DNA Modification Methylases - genetics; DNA Repair Enzymes - genetics; Functional; Glioma - diagnostic imaging; Glioma - genetics; Humans; Magnetic Resonance Imaging - methods; Male; Middle Aged; Neural Networks, Computer; Promoter Regions, Genetic; Reproducibility of Results; Sensitivity and Specificity; Tumor Suppressor Proteins - genetics
• DOI: 10.3174/ajnr.A7029
• ISSN: 0195-6108; 1936-959X

( ) promoter methylation confers an improved prognosis and treatment response in gliomas. We developed a deep learning network for determining promoter methylation status using T2 weighted Images (T2WI) only. Brain MR imaging and corresponding genomic information were obtained for 247 subjects from The Cancer Imaging Archive and The Cancer Genome Atlas. One hundred sixty-three subjects had a methylated promoter. A T2WI-only network ( -net) was developed to determine promoter methylation status and simultaneous single-label tumor segmentation. The network was trained using 3D-dense-UNets. Three-fold cross-validation was performed to generalize the performance of the networks. Dice scores were computed to determine tumor-segmentation accuracy. The -net demonstrated a mean cross-validation accuracy of 94.73% across the 3 folds (95.12%, 93.98%, and 95.12%, [SD, 0.66%]) in predicting methylation status with a sensitivity and specificity of 96.31% [SD, 0.04%] and 91.66% [SD, 2.06%], respectively, and a mean area under the curve of 0.93 [SD, 0.01]. The whole tumor-segmentation mean Dice score was 0.82 [SD, 0.008]. We demonstrate high classification accuracy in predicting promoter methylation status using only T2WI. Our network surpasses the sensitivity, specificity, and accuracy of histologic and molecular methods. This result represents an important milestone toward using MR imaging to predict prognosis and treatment response.